centralized database configuration

7 files changed, 37 insertions, 10 deletions

diff --git a/Rakefile b/Rakefile
index ba06640..e585ca6 100644
--- a/Rakefile
+++ b/Rakefile
@@ -10,7 +10,7 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
+		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets", "do_sqlite3", "do_postgres"].each do |dep|
 			gem.add_dependency dep
 		end
 		gem.add_development_dependency "cucumber"
diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index c5d162a..25ae4cb 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -39,6 +39,7 @@ module OpenTox
 			end
 			
 			def self.create_model(params)
+				LOGGER.debug params
 				@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
 			end
 
diff --git a/lib/compound.rb b/lib/compound.rb
index 562baaa..56646c0 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -21,20 +21,20 @@ module OpenTox
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
 				@uri = params[:uri]
-				if params[:uri].match(/InChI/) # shortcut for IST services
+				case params[:uri]
+				when /ambit/ # Ambit does not deliver InChIs reliably
+					smiles = RestClient.get @uri, :accept => 'chemical/x-daylight-smiles'
+					@inchi = obconversion(smiles,'smi','inchi')
+				when /InChI/ # shortcut for IST services
 					@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
 				else
 					@inchi = RestClient.get @uri, :accept => 'chemical/x-inchi'
-					# AMBIT does not provide InChIs
-					#smiles = RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
-					#@inchi = obconversion(smiles,'smi','inchi')
 				end
 			end
 		end
 
 		# Get the (canonical) smiles
 		def smiles
-			#RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
 			obconversion(@inchi,'inchi','can')
 		end
 
diff --git a/lib/tasks/config.rb b/lib/config/config_ru.rb
index 3720ef3..3720ef3 100644
--- a/lib/tasks/config.rb
+++ b/lib/config/config_ru.rb
diff --git a/lib/environment.rb b/lib/environment.rb
index a9d0797..fedc3cf 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -2,7 +2,7 @@ require 'logger'
 # set default environment
 ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
 
-# load configuration
+# load/setup configuration
 basedir = File.join(ENV['HOME'], ".opentox")
 config_dir = File.join(basedir, "config")
 config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
@@ -19,6 +19,26 @@ else
 	puts "Please edit #{config_file} and restart your application."
 	exit
 end
+
+# database
+if @@config[:database]
+	['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types'].each{|lib| require lib }
+	case @@config[:database][:adapter]
+	when /sqlite/i
+		db_dir = File.join(basedir, "db")
+		FileUtils.mkdir_p db_dir
+		DataMapper::setup(:default, "sqlite3://#{db_dir}/opentox.sqlite3")
+	else
+		DataMapper.setup(:default, { 
+				:adapter  => @@config[:database][:adapter],
+				:database => @@config[:database][:database],
+				:username => @@config[:database][:username],
+				:password => @@config[:database][:password],
+				:host     => @@config[:database][:host]})
+	end
+end
+
+# logging
 logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
 LOGGER = Logger.new(logfile,'daily') # daily rotation
 LOGGER.level = Logger::DEBUG
diff --git a/lib/task.rb b/lib/task.rb
index 24bd944..9e60c2e 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -10,7 +10,7 @@ module OpenTox
 		end
 
 		def self.create
-			uri = RestClient.post @@config[:services]["opentox-task"], nil
+			uri = RestClient.post @@config[:services]["opentox-task"], {}
 			Task.new(uri)
 		end
 
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index c803a5c..36ae17b 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "1.2.6"
+  s.version = "1.2.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2010-01-31}
+  s.date = %q{2010-02-02}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
   s.executables = ["opentox-install-debian.sh", "yaml2owl.rb"]
@@ -62,6 +62,8 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<dm-more>, [">= 0"])
       s.add_runtime_dependency(%q<dm-core>, [">= 0"])
       s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"])
+      s.add_runtime_dependency(%q<do_sqlite3>, [">= 0"])
+      s.add_runtime_dependency(%q<do_postgres>, [">= 0"])
       s.add_development_dependency(%q<cucumber>, [">= 0"])
     else
       s.add_dependency(%q<sinatra>, [">= 0"])
@@ -75,6 +77,8 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<dm-more>, [">= 0"])
       s.add_dependency(%q<dm-core>, [">= 0"])
       s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
+      s.add_dependency(%q<do_sqlite3>, [">= 0"])
+      s.add_dependency(%q<do_postgres>, [">= 0"])
       s.add_dependency(%q<cucumber>, [">= 0"])
     end
   else
@@ -89,6 +93,8 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<dm-more>, [">= 0"])
     s.add_dependency(%q<dm-core>, [">= 0"])
     s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
+    s.add_dependency(%q<do_sqlite3>, [">= 0"])
+    s.add_dependency(%q<do_postgres>, [">= 0"])
     s.add_dependency(%q<cucumber>, [">= 0"])
   end
 end